Atlantis: The Apocalypse
by MysticMaiden 18
Summary: Sigma has finally crossed the line between life and death. Uncovering the runes of an ancient civilisation, he uncovered a deadly secret, buried beneathan the ancient runes.A secret which will lead X further into the long road of darkness, death, and betr
1. Chapter 1

This is my second MegaMan fiction. I want to thank my readers and reviewers, for my first mega man, and my Yugioh fiction. Due to your support I was able to write those fictions.

Your support is greatly appreciated; hope you like this fiction as well. Please REVIEW and tell me what you think and if I should continue it or not.

_Atlantis: The Apocalypse_

_Chapter 1_

_A History Untold_

_The Fall of Atlantis_

Wiping the sweat of his brow he looked around at the rocky walls. Even though he was a biologist excavations for ancient artifacts were his passion, to discover the unknown of something not under the microscope.

Professor Michael, he turned around to see one of the diggers calling out to him.

Blinking he tried to see as he followed his co-worker through the dust. He had a hard time maintaining his excitement they were on a break on one of the greatest discoveries in history. But what he didn't know it will be also a discovery that will open one of the gates to hell, and the end to the life they once knew.

Staring through the eye piece of the microscope he wondered what the thing they had discovered was. Returning the slide he left the lab and went home. He couldn't help but worry at the pathogen he had found in the mummified corpse. A whole city was buried under the sand, after a long search the only clue that anyone lived was the mummified corpse.

It was branded with crosses and writings which seemed to be written in blood. But scientific curiosities overcame spiritual suppuration. He didn't believe in things such as bad luck, curses or the gods' anger. But their was a nagging feeling shouting at the back of his mind to burn everything that they had found.

He sighed as he locked the apartment doors, and went to find something to eat in the kitchen. He grimaced as he opened the fridge, a smell of rotten food reached his nose. Quickly closing it he knew that he needed to clean the fridge soon but he didn't know it was this bad.

Rubbing his nose he tried to get rid of the neusting smell. Staring out of the window he looked at the city below. Even though it was only 186 A.C. Atlantis had reached a level of advanced technology, then any other nation in the world. Nations where people still lived in wooden houses and died from simple diseases such as the flue and chicken pox, diseases which they had discovered cures and vaccines more then 50 years ago.

Some of the people were against Atlantis cutting off itself from the rest of the world; he was one of the leaders of organizations that demanded of the government to declare itself to the world. But the government still kept its stand, they were afraid of what other nations will do when they see all their nations riches. They argued that the rest of the world wasn't prepared to be introduced to such technology.

He thought back with sadness as he remembered the embassy that they had send, only one survivor had returned the rest were brutally murdered and copse were hung after they were looted by a race that called themselves Vikings. This had sent them hurtling backwards, years of work was almost lost. Peoples fear rose higher then before and more and more people ran to the government asking that their isolation to remain.

He too was starting to doubt that the rest of mankind was prepared to deal with what they had to offer. It was estimated that it would take thousands of years for the rest of the human society to reach their level of technological advancement. He and the others agreed to wait and give a small nudge here and their, small in not to alert anyone of their existence, but enough to give a satisfactory effect.

He looked at the clock and found that he needed to go see how the translations with the coffins' writings. Reaching the museum he headed to search for the office. Hearing a voice calling his name, he turned around to see Kin running in his direction. He smiled at the young boys' enthusiasm; he was very dedicated to his work, and had a promising future.

Kin was almost jumping up and down with joy, he grinned at the professor as he tried to regain his composer. He felt himself swell with pride as he looked at the professor he had always admired him and the discoveries he had a hand in, it was quite an honor to work on the same project with someone like him.

We discovered what the writings said, its very exceptional sir.

Never seen something like this before.

Michael smiled softly at the young man who had turned around and headed rather hurriedly toward the lab. But as he came closer to were the coffin was being kept he couldn't help but shiver he felt that something evil was present.

Shaking his head he gave a small laugh at his foolishness he is a man of science not a spiritual believer in the unknown. Everything had a scientific base, ghosts and evil spirits do not exist. Kin opened the door unaware of the dilemma the professor was going though.

Michael suddenly felt a breath of cool air passing by; as he stared into the room he reluctantly followed. Staring at the projections of the translated writings, he smiled forgetting his worries he soon got immersed in the translations.

The writings told of an evil spirit sent by the gods in a moment of anger to punish their people. It had eaten away the flesh of the living and had weakened the earth. But the man they had found in the coffin had lead them away were they had built the city underground.

But why was no evidence was found that anyone lived their, he guessed that they had abandoned it a while later but why that was the question, and why was he only one buried their.

He walked out of the museum wondering on what he had found. They had more writings of some kind of warning; they had gathered that the evil sprit was representing some kind of diseases.

Instead of heading home he headed toward the ocean, his late mother was a seer, even though he was a man of science he still believe in his mother's visions, and abilities. He had inherited her powers but more of a six senses the only visions he had were a sort of warnings, they had ceased after the vision he had of his mother's death.

He had suppressed his abilities to a certain extent, but not enough to suppress his six sense. His senses were now warning him of an upcoming danger, and a sense that this would be one of the last few days that Atlantis would find peace.

_Two weeks Later…_

He stood at the outskirts of the city listening to the screams of the dying. He felt tears falling from his eyes as he wondered how things could get this way. They had isolated the sick, placing as much people as they could to delay their pain, as they awaited their death.

He now truly understood the meaning of the evil spirit they had found in the translations. The disease had escaped and spread through the population like fire. No child, no animal or plant was spared. The earth had starting to break away; no one could understand how the virus had such an effect.

He looked at his hands and saw them drenched in blood; he had helped in this discovery costing his people their lives. But his instincts as a seer told him otherwise; it needed to be one Atlantis was doomed since the day they had build their first building they were intruders in this time period, the world was not prepared for them yet.

Embracing his seer abilities, he turned around his life wasn't here to help the survivors, nor try to fix the past. He left the island and watched it break away and sink into the dark sea burying its secrets. But Atlantis will once more resurface and join history as the site where the Apocalypse began once more.

This time he was prepared he will not allow history to repeat itself, using his abilities he disappeared to the future where the saver of mankind was being born. MegaMan X would be the only being that would be immune to the virus and will able to save and rewrite the future of the second Apocalypse saving the loss once lost in the second rising of darkness.

He appeared 5,000 years later where Dr. Light has started to build his most powerful creation MegaMan.

_To Be Continued_

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_I know that their was nothing on X in this chapter, but I promise that he will appear in the next chapter._

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	2. Chapter 2

I want to send thanks to all my readers and reviewer.

Hope you would like this chapter as well.

Tell me what you think so far, should I keep going.

_**Atlantis: The Apocalypse**_

_**Chapter 2**_

_**A glimpse into the future**_

X watched the ruined planes in front of him, no sign of any living being, even reploids could be seen, and they have become a very rare sight these days. The plague had brought its toll on everyone.

He heard footsteps behind him, but he continued to watch his surroundings ignoring who was approach. The approaching reploid moved his scarf from his face as it blew with the wind, placing his shield into the ground; he leaned against it and stared at his brother.

It hurt him to see his brother this way, the innocent youth he knew was now gone, killed by the harsh realties of the world they lived in. He was himself shaken from what he had seen, he couldn't look at the mirror without seeing the haunted dark look in his eyes without flinching and looking away.

He could only imagine what his brother had gone through, who was awake from the beginning. He slightly flinched when his brothers' gaze was directed at him. They were totally empty devoid of any emotions; they were now only cold dark abysses. When they were directed toward you, it would give you a sense of being judged they replayed the horrors he had seen.

_X prove_

X looked sadly as he watched Protoman uncomfortably flinch as he looked at him, he didn't blame him, and he couldn't even look into his reflection without feeling a slight fear. Fear he wondered that word seemed strange to him, he shrugged he appreciated and was somehow grateful that his brother and sister remained with him despite their discomfort. The few that were on his team were too scared to be around him unless it's necessary.

He could feel guilt every time he looked at Protoman or Roll; he had woken them up from a peaceful slumber to the horrors of the surrounding world. Even though he didn't want to admit he wanted companionship, all his friends had died and those few who were alive were too scared of the cold reploid that was somehow immune to the virus. On finding their capsules he was too ecstatic too let the chance of having a real family back.

_Protoman Prove_

He redirected his gaze to the ruined plains once more; leaving Protoman with a sense of guilt knowing that he was the one caused X to look away. He sighed even though X thought h was unreadable to those who are around him; he was wrong as soon as you get to know him he could be read like a book by watching his body movements.

The last of the northern islands had sunk, we only found some of the survivors, but many were too infected and they died. X nodded but remained quite Protoman sighed and turned around to leave and wait for any instructions his brother may have, but he stopped in his tracks when he heard a voice.

"Protoman, what would you do if you were given a chance to change everything"

"Changing the past, it would be tricky if time travel was possible, do you have something in mind".

Protoman stood waiting for his brothers to speak.

"You know, every time I see a reploid or any of the remaining humans die by disease or be killed by a mad reploid, I let it go, and don't try to stop it, saying to myself what is ones life compared too many.''

"But is it true, I once believed that every life is precious and deserves a chance to repent but as years passed all you could do was watch them die, and kill off those who where dying to try to reduce the infection, no matter that the infected individual was a victim himself."

"Such childless believes have no pace in this world".

All what Protoman could do was stand and listen to his brothers words. He could feel his heart brake once more, to know and see but to hear these words from X mouth showed the extent of the damage to the x-hunters soul.

Roll who has arrived a few minutes ago walked up to X and pulled him into a hug she wanted to push his daemons away and get her older brother back, even though she knew that it probably wont be possible if they continued to live like this. Surprised to feel an arm wrap around her waist she smiled a sad smile.

It was time she thought "X there is something I need to show you."

_A few miles away_

They had arrived to the place were X had found their capsules; this was a secret neither Doctor Light knew about. What wasn't known that Dr.light did not build X alone but he had outside help. He was known as a Michael he had appeared out of n where and offered to help X Dr. Light to rebuild X, even tough he was suspicious at the stranger they soon became best of friends.

She remembered when he first approached her that day.

_Flash back_

_She had let her hair loose and stood feeling the wind move her hair. She had grown more quite after X died and spend hr time alone. Staring back sadly at the lab she, she knew that Dr. Light was rebuilding her brother, but she doubted that he will be the same he may have X memories but he was a new individual, probably he will have his own different personality. _

_She had accepted her brothers' death, but she considered Meg man X as a new addition, she won't condemn him to the name oh his predecessor. She then felt a hand on her shoulder,_

"_How are you doing Roll"?_

_Roll stared back and smiled sadly at the doctor_

"_Ill be fine, thank you. Where's father is he still inside."_

_Nodding his head, roll stared back and sighed it seems that Dr.light was not eating well again these days, his health was slowly detrating. Heading toward the lab she prepared herself to face another argument and pull Dr.light from his lab. _

_Roll their something I need to tell you. _

_He continued to tell Roll about his history and life in Atlantis. As the hour past Roll feared that the doctor had gone made like wily and started to back away. He quickly moved and took hold of her hand. I want to show you proof roll I haven't gone made like wily. _

_Looking into his eyes all what could she was sincerity no madness could be seen in his gaze or poster, but wasn't it the same with Dr. Wily, she sighed what did she have to loose. She nodded and followed him._

_Two hours later_

_She stood at the same place Michael had stood watching Atlantis sink, she knew that this wasn't a hologram he had shown her the blue prints and even tested it. So everything he said was true, she turned around and watched Michael's sad gaze as he stared at his home lost in memories as it broke down and fell into the ocean._

_"I believe you, but what do you want from me now."_

_"Roll, the only thing I want from you is to keep show this to X one day"._

_"But aren't you going to activate him in a matter of weeks."_

_"No, Roll this time isn't where X fate les we have agreed to place him, you and Protoman in a capsule as well."_

_"I will, but I would be doing it for him not you doctor."_

_He nodded I didn't expect anything else", nodding he took them back to their time._

_----------------------------------------------------------------------------------------------------------------_

_End of flash back._

I want to tell you about something I have been hiding even before we entered the capsule, the history of Atlantis, and our last hope to rewrite the past.

_So what do you think?_

_Hope you liked it._

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